Type I, or insulin-dependent, diabetes mellitus (IDDM) and other organ- specific autoimmune diseases are common in developed-country populations-10-15% of the population may suffer from one or more of these disorders. IDDM itself has a prevalence approaching 1% and the morbidity caused by improper glucose control imposes large costs on both the individual patient and society. Although IDDM has a substantial genetic component, the large genetic variation in human populations has made it difficult to study. We have therefore genetically dissected IDDM in the BioBreeding (BB) rat model of IDDM by identifying three genetic factors with major effects on IDDM in our crosses: 1ddm1/Lyp on chromosome 4 and Iddm2 (rat MHC) on chromosome 2o confer susceptibility, while the Fischer rat allele of Iddm3 confers protection against IDDM in a genetic background of Iddm1 and Iddm2 susceptibility alleles. We have made great progress toward cloning the Iddm1/Lyp gene, as described in the PPG overview and Project 2 application. Our primary goal is to understand the molecular nature of the effects of Iddm1/Lyp and Iddm3 on the development of IDDM. For this renewal, we build on our previous successful work and take advantage of the tremendous recent advances in genomics. Our specific proposals are as follows" 1. Complete the positional cloning of the Iddm1/Lyp gene. The positional cloning of Lyp is in the final gene identification phase. In this collaboration with project 1, we will apply our genomic sequencing and associated informatics expertise to (a) complete the sequencing of the entire approximately 800 kb Lyp region in the rat and its orthologous region in the mouse in order to completely identify the genes in the recombinationally-defined subinterval that contains Lyp and (b) as necessary, resequence regions of that interval in the BB-DP (Lyp/Lyp) and wild-type rat strains in order to identify the sequence polymorphism causing the Lyp defect. 2. Positionally clone the Iddm3 gene. In this collaboration with projects 1 and 3, we will assist in the positional cloning of Iddm3. The positional cloning expertise and reagents gained through numerous projects described below in addition to the successful work on Lyp has been transferred to projects 1 and 3; thus, as above, our contribution to this aim will be to make use of our large-scale genomic sequencing expertise and infrastructure to (a) completely sequence the genomic regions containing the rat Iddm3 gene and its mouse ortholog and to (b) perform such large- scale resequencing as required to identify the Iddm3 sequence polymorphism. 3. Construct transgenic rats to prove gene identity. As necessary, prove the identity of the genes identified in aims 1 and 2 by constructing single transgenic rats carrying the wild-type allele of Lyp and Iddm3 on an otherwise susceptible genetic background.